id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1840 Session restore with BILD objects: Unable to restore objects of AtomicShapeDrawing class kovacs.bertalan@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-47-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.8 (2018-12-17) Description Unable to save chimerax session or render png image file from the attached BILD file. Log: Startup Messages --- note | Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 338, in __init__ self.init_available_from_cache(logger) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 445, in init_available_from_cache abc.load_from_cache() File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 61, in load_from_cache b = _build_bundle(d) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 242, in _build_bundle keywords = _extract_extra_keywords(keywords) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/installed.py"", line 270, in _extract_extra_keywords all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX > open c1.0_drawing.bild Opened BILD data containing 14 objects > save session ""/HDD/Dokumentumok/PhD/PROJECTS/tandem PDZ/analyses/15_redo_evaluation/fit_tandem_ensembles/fit_to_template/explicit_analyses/ligand_alignment/session.cxs"" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py"", line 791, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py"", line 564, in file_save_cb self.save_dialog.display(self, session) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2587, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 917, in save_session save(session, filename, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/io.py"", line 198, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 500, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 265, in process return copy_state(data, convert=self._add_obj) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 174, in copy_state return _copy(data) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 168, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 168, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 172, in _copy return convert(data) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 240, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) RuntimeError: Unable to restore objects of AtomicShapeDrawing class in ChimeraX-Atomic bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of AtomicShapeDrawing class in ChimeraX-Atomic bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. > save session ""/HDD/Dokumentumok/PhD/PROJECTS/tandem PDZ/analyses/15_redo_evaluation/fit_tandem_ensembles/fit_to_template/explicit_analyses/ligand_alignment/session.cxs"" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py"", line 791, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py"", line 564, in file_save_cb self.save_dialog.display(self, session) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2587, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 917, in save_session save(session, filename, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/io.py"", line 198, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 500, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 265, in process return copy_state(data, convert=self._add_obj) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 174, in copy_state return _copy(data) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 168, in _copy items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 168, in items = [_copy(o) for o in data] File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/state.py"", line 172, in _copy return convert(data) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 240, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) RuntimeError: Unable to restore objects of AtomicShapeDrawing class in ChimeraX-Atomic bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of AtomicShapeDrawing class in ChimeraX-Atomic bundle because the class name is not listed in the name to class table for session restore File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. OpenGL version: 4.5 (Core Profile) Mesa 18.2.8 OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) OpenGL vendor: Intel Open Source Technology Center File attachment: c1.0_drawing.bild }}} [attachment:""c1.0_drawing.bild""] " defect closed normal 1.0 Depiction fixed all ChimeraX